title: Diplotyper: diplotype-based association analysis.
abstract: BACKGROUND
  It was previously reported that an association analysis based on haplotype clusters increased power over single-locus tests, and that another association test based on diplotype trend regression analysis outperformed other, more common association approaches. We suggest a novel algorithm to combine haplotype cluster- and diplotype-based analyses.
  
  
  METHODS
  Diplotyper combines a novel algorithm designed to cluster haplotypes of interest from a given set of haplotypes with two existing tools: Haploview, for analyses of linkage disequilibrium blocks and haplotypes, and PLINK, to generate all possible diplotypes from given genotypes of samples and calculate linear or logistic regression. In addition, procedures for generating all possible diplotypes from the haplotype clusters and transforming these diplotypes into PLINK formats were implemented.
  
  
  RESULTS
  Diplotyper is a fully automated tool for performing association analysis based on diplotypes in a population. Diplotyper was tested through association analysis of hepatic lipase (LIPC) gene polymorphisms or diplotypes and levels of high-density lipoprotein (HDL) cholesterol.
  
  
  CONCLUSIONS
  Diplotyper is useful for identifying more precise and distinct signals over single-locus tests.
authors.affiliation: Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea.
authors.forename: Sunshin
authors.initials: S
authors.lastname: Kim
authors.forename: KyungChae
authors.initials: K
authors.lastname: Park
authors.forename: Chol
authors.initials: C
authors.lastname: Shin
authors.forename: Nam H
authors.initials: NH
authors.lastname: Cho
authors.forename: Jeong-Jae
authors.initials: JJ
authors.lastname: Ko
authors.forename: InSong
authors.initials: I
authors.lastname: Koh
authors.forename: KyuBum
authors.initials: K
authors.lastname: Kwack
mesh_terms: D000465:Algorithms; D008076:Cholesterol, HDL / Q000097:blood*; D003430:Cross-Sectional Studies; D005260:Female; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium; D008049:Lipase / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012984:Software
chemical_list: D008076:Cholesterol, HDL; C504173:LIPC protein, human; D008049:Lipase